Add shell module and bootstrap fixes

modules/system/shell.nix

@@ -0,0 +1,39 @@
+{ pkgs, ... }:
+
+let
+  shellInitScript =
+    builtins.replaceStrings
+      [ "@ATUIN@" "@STARSHIP@" "@BASHPREEXEC@" ]
+      [
+        "${pkgs.atuin}/bin/atuin"
+        "${pkgs.starship}/bin/starship"
+        "${pkgs.bash-preexec}/share/bash/bash-preexec.sh"
+      ]
+      (builtins.readFile ../../scripts/shell-init.sh);
+in
+{
+
+  environment.systemPackages = [
+    pkgs.atuin
+    pkgs.bat
+    pkgs.eza
+    pkgs.fzf
+    pkgs.starship
+    pkgs.ugrep
+    pkgs.zoxide
+  ];
+
+  # Use Ghostty as the default terminal emulator.
+  environment.sessionVariables = {
+    TERMINAL = "${pkgs.ghostty}/bin/ghostty";
+    DEFAULT_TERMINAL = "${pkgs.ghostty}/bin/ghostty";
+  };
+
+  programs.bash = {
+    enable = true;
+    interactiveShellInit = shellInitScript;
+    loginShellInit = shellInitScript;
+    promptInit = ""; # avoid overriding Starship prompt
+  };
+  
+}